Alexander T.J. Lee
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View article: Cell-free DNA methylome and fragmentome analysis for disease relapse monitoring in patients with Ewing Sarcoma
Cell-free DNA methylome and fragmentome analysis for disease relapse monitoring in patients with Ewing Sarcoma Open
Summary Liquid biopsies and cell-free DNA (cfDNA) offer minimally invasive methods for the diagnosis and monitoring of Ewing Sarcoma (EwS). EwS have a low tumour mutational burden and their detection with plasma cfDNA is challenging. We hy…
View article: Supplementary Figure S3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S3. Expression of matrisome proteins in a desmoid tumour cohort (n=37) split into 3 groups based on the % tumour content.
View article: Figure 5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Figure 5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Proteoglycan protein expression identifies a high-risk STS group. A, Summary of log-rank tests used to assess significant associations of matrisome-related gene sets with LRFS, MFS, and OS. The scores for each patient were obtained by taki…
View article: Figure 1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Figure 1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
The matrisome and adhesome landscape of soft tissue sarcomas (STS). A, Annotated heatmap illustrating the unsupervised clustering (Pearson’s correlation distance) of 302 matrisome and adhesome components in the STS cohort. Top annotation p…
View article: Supplementary Table S13 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S13 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S13. Summary of univariable (UVA) and multivariable (MVA) Cox regression analyses assessing the association of clinicopathological factors and ssGSEA-derived proteoglycan score with overall survival (OS).
View article: Supplementary Table S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S1: Matrisome and adhesome proteins identified across the soft tissue sarcoma (STS) cohort. Table showing annotation of proteins according to matrisome and integrin adhesome databases and the breakdown into functional m…
View article: Supplementary Table S4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S4: Statistical comparisons between histological subtypes in cluster 1 (C1).
View article: Supplementary Figure S6 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S6 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S6. Identification of LCP1 as a candidate prognostic factor in LMS.
View article: Table 1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Table 1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Clinicopathological characteristics of the cohort.
View article: Supplementary Table S2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S2: Matrisome and adhesome cluster membership.
View article: Supplementary Table S5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S5. Summary of multivariable (MVA) analyses assessing association of clinicopathological factors and LCP1 tertiles with local recurrence-free survival (LRFS) and overall survival (OS). Clinicopathological factors which …
View article: Supplementary Figure S5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S5 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S5. Assessment of leiomyosarcoma (LMS) extracellular matrix (ECM) solution and its effects of cell migration.
View article: Supplementary Table S6 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S6 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S6: Clinicopathological characteristics of n=39 dedifferentiated liposarcoma (DDLPS). Summary features of the cohort. For continuous variables, the median, minimum (min) and maximum (max) values are indicated. For categ…
View article: Supplementary Table S12 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S12 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S12. Summary of univariable (UVA) and multivariable (MVA) Cox regression analyses assessing the association of clinicopathological factors and median proteoglycan score with overall survival (OS).
View article: Supplementary Table S8 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S8 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S8: Summary of univariable (UVA) Cox regression analyses assessing the association of clinicopathological factors and dedifferentiated liposarcoma (DDLPS) subgroups with local recurrence-free survival (LRFS), overall su…
View article: Supplementary Figure S4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S4. Differentially expressed matrisome proteins in synovial sarcoma (SS) cases (n=42) that either received preoperative treatment or were untreated.
View article: Supplementary Methods S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Methods S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplemental Methods
View article: Supplementary Figure S7 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S7 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S7. Clinical characterisation of DDLPS subgroups.
View article: Supplementary Figure S2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S2. Validation of MMP14 expression in undifferentiated pleomorphic sarcoma (UPS), dedifferentiated liposarcoma (DDLPS) and leiomyosarcoma (LMS) by immunohistochemistry (IHC).
View article: Supplementary Table S7 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S7 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S7: Summary of statistical tests to assess the association between clinicopathological features and dedifferentiated liposarcoma (DDLPS) subgroups.
View article: Supplementary Table S9 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S9 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S9: Summary of multivariable (MVA) Cox regression analyses assessing the association of clinicopathological factors and dedifferentiated liposarcoma (DDLPS) subgroups with local recurrence-free survival (LRFS), overall …
View article: Supplementary Table S10 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S10 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S10. Clinicopathological characteristics of n=92 undifferentiated pleomorphic sarcoma (UPS) and dedifferentiated liposarcoma (DDLPS) cases. Summary features of the cohort. For continuous variables, the median, minimum (…
View article: Supplementary Figure S8 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S8 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S8. Association of the proteoglycan gene expression score with survival outcomes in The Cancer Genome Atlas sarcoma (TCGA- SARC) cohort.
View article: Supplementary Table S11 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S11 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S11. Statistical association of clinicopathological features with proteoglycan groups.
View article: Figure 4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Figure 4 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Identification, biological and clinical characterization of DDLPS subgroups. A, Heatmap showing the supervised clustering of 57 differentially expressed matrisome and adhesome proteins (DEPs) uniquely upregulated in each DDLPS subgroup. Bl…
View article: Supplementary Figure S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Figure S1 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Figure S1. The matrisome and adhesome profiles in soft tissue sarcoma (STS).
View article: Figure 2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Figure 2 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Matrisome and adhesome networks in STS. A, Heatmap showing a similarity matrix of Pearson’s correlation coefficients for all pairwise comparisons of matrisome and adhesome proteins. Heatmap is split into three clusters (C1, C2, and C3) ide…
View article: Figure 3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Figure 3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Generation and characterization of LMS ECM solution. A, A workflow to generate decellularized ECM LMS scaffolds from fresh frozen LMS tumors by extensive washes with detergent and generation of LMS ECM solution by incubating dried scaffold…
View article: Supplementary Table S3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas
Supplementary Table S3 from Clinical Implications and Molecular Features of Extracellular Matrix Networks in Soft Tissue Sarcomas Open
Supplementary Table S3: Reactome enriched pathways in soft tissue sarcoma (STS) matrisome and adhesome clusters. Tables for each cluster showing enriched term description and false discovery rate (FDR). Top 10 hits with FDR < 0.001 are sho…